A radial differential mobility analyzer for the size-classification of gas-phase synthesized nanoparticles at low pressures

Differential mobility analyzers (DMAs) are commonly used to generate monodisperse nanoparticle aerosols. Commercial DMAs operate at quasi-atmospheric pressures and are therefore not designed to be vacuum-tight. In certain particle synthesis methods, the use of a vacuum-compatible DMA is a requirement as a process step for producing high-purity metallic particles. A vacuum-tight radial DMA (RDMA) has been developed and tested at low pressures. Its performance has been evaluated by using a commercial NANO-DMA as the reference. The performance of this low-pressure RDMA (LP-RDMA) in terms of the width of its transfer function is found to be comparable with that of other NANO-DMAs at atmospheric pressure and is almost independent of the pressure down to 30 mbar. It is shown that LP-RDMA can be used for the classification of nanometer-sized particles (5-20 nm) under low pressure condition (30 mbar) and has been successfully applied to nanoparticles produced by ablating FeNi at low pressures.

Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis

Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies. In human, six distinct thiolases have been identified. Each of these thiolases is different from the other with respect to sequence, oligomeric state, substrate specificity and subcellular localization. Four sequence fingerprints, identifying catalytic loops of thiolases, have been described. In this study genome searches of two mycobacterial species (Mycobacterium tuberculosis and Mycobacterium smegmatis), were carried out, using the six human thiolase sequences as queries. Eight and thirteen different thiolase sequences were identified in M. tuberculosis and M. smegmatis, respectively. In addition, thiolase-like proteins (one encoded in the Mtb and two in the Msm genome) were found. The purpose of this study is to classify these mostly uncharacterized thiolases and thiolase-like proteins. Several other sequences obtained by searches of genome databases of bacteria, mammals and the parasitic protist family of the Trypanosomatidae were included in the analysis. Thiolase-like proteins were also found in the trypanosomatid genomes, but not in those of mammals. In order to study the phylogenetic relationships at a high confidence level, additional thiolase sequences were included such that a total of 130 thiolases and thiolase-like protein sequences were used for the multiple sequence alignment. The resulting phylogenetic tree identifies 12 classes of sequences, each possessing a characteristic set of sequence fingerprints for the catalytic loops. From this analysis it is now possible to assign the mycobacterial thiolases to corresponding homologues in other kingdoms of life. The results of this bioinformatics analysis also show interesting differences between the distributions of M. tuberculosis and M. smegmatis thiolases over the 12 different classes. (C) 2014 Elsevier Ltd. All rights reserved.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

Framework for morphometric classification of cells in imaging flow cytometry

Imaging flow cytometry is an emerging technology that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy. It allows high-throughput imaging of cells with good spatial resolution, while they are in flow. This paper proposes a general framework for the processing/classification of cells imaged using imaging flow cytometer. Each cell is localized by finding an accurate cell contour. Then, features reflecting cell size, circularity and complexity are extracted for the classification using SVM. Unlike the conventional iterative, semi-automatic segmentation algorithms such as active contour, we propose a noniterative, fully automatic graph-based cell localization. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using custom fabricated cost-effective microfluidics-based imaging flow cytometer. The proposed system is a significant development in the direction of building a cost-effective cell analysis platform that would facilitate affordable mass screening camps looking cellular morphology for disease diagnosis. Lay description In this article, we propose a novel framework for processing the raw data generated using microfluidics based imaging flow cytometers. Microfluidics microscopy or microfluidics based imaging flow cytometry (mIFC) is a recent microscopy paradigm, that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy, which allows us imaging cells while they are in flow. In comparison to the conventional slide-based imaging systems, mIFC is a nascent technology enabling high throughput imaging of cells and is yet to take the form of a clinical diagnostic tool. The proposed framework process the raw data generated by the mIFC systems. The framework incorporates several steps: beginning from pre-processing of the raw video frames to enhance the contents of the cell, localising the cell by a novel, fully automatic, non-iterative graph based algorithm, extraction of different quantitative morphological parameters and subsequent classification of cells. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using cost-effective microfluidics based imaging flow cytometer. The cell lines of HL60, K562 and MOLT were obtained from ATCC (American Type Culture Collection) and are separately cultured in the lab. Thus, each culture contains cells from its own category alone and thereby provides the ground truth. Each cell is localised by finding a closed cell contour by defining a directed, weighted graph from the Canny edge images of the cell such that the closed contour lies along the shortest weighted path surrounding the centroid of the cell from a starting point on a good curve segment to an immediate endpoint. Once the cell is localised, morphological features reflecting size, shape and complexity of the cells are extracted and used to develop a support vector machine based classification system. We could classify the cell-lines with good accuracy and the results were quite consistent across different cross validation experiments. We hope that imaging flow cytometers equipped with the proposed framework for image processing would enable cost-effective, automated and reliable disease screening in over-loaded facilities, which cannot afford to hire skilled personnel in large numbers. Such platforms would potentially facilitate screening camps in low income group countries; thereby transforming the current health care paradigms by enabling rapid, automated diagnosis for diseases like cancer.

A bioregional classification of the continental shelf of northeastern North America for conservation analysis and planning based on representation

Understanding how well National Marine Sanctuaries and other marine protected areas represent the diversity of species present within and among the biogeographic regions where they occur is essential for assessing their conservation value and identifying gaps in the protection of biological diversity. One of the first steps in any such assessment should be the development of clearly defined and scientifically justified planning boundaries representing distinct oceanographic conditions and faunal assemblages. Here, we propose a set of boundaries for the continental shelf of northeastern North America defined by subdivisions of the Eastern Temperate Province, based on a review and synthesis (i.e. meta-analysis) of the scientific literature. According to this review, the Eastern Temperate Province is generally divided into the Acadian and Virginian Subprovinces. Broad agreement places the Scotian Shelf, Gulf of Maine, and Bay of Fundy within the Acadian Subprovince. The proper association of Georges Bank is less clear; some investigators consider it part of the Acadian and others part of the Virginian. Disparate perspectives emerge from the analysis of different groups of organisms. Further, while some studies suggest a distinction between the Southern New England shelf and the rest of the Mid-Atlantic Bight, others describe the region as a broad transition zone with no unique characteristics of its own. We suggest there exists sufficient evidence to consider the Scotian Shelf, Gulf of Maine, Georges Bank, Southern New England, and Southern Mid-Atlantic Bight as distinct biogeographic regions from a conservation planning perspective, and present a set of proposed mapped boundaries. (PDF contains 23 pages.)

Survey report of NOAA Ship McArthur II cruises AR-04-04, AR-05-05 and AR-06-03: Habitat classification of side scan sonar imagery in support of deep-sea coral/sponge explorations at the Olympic Coast National Marine Sanctuary

Habitat mapping and characterization has been defined as a high-priority management issue for the Olympic Coast National Marine Sanctuary (OCNMS), especially for poorly known deep-sea habitats that may be sensitive to anthropogenic disturbance. As a result, a team of scientists from OCNMS, National Centers for Coastal Ocean Science (NCCOS), and other partnering institutions initiated a series of surveys to assess the distribution of deep-sea coral/sponge assemblages within the sanctuary and to look for evidence of potential anthropogenic impacts in these critical habitats. Initial results indicated that remotely delineating areas of hard bottom substrate through acoustic sensing could be a useful tool to increase the efficiency and success of subsequent ROV-based surveys of the associated deep-sea fauna. Accordingly, side scan sonar surveys were conducted in May 2004, June 2005, and April 2006 aboard the NOAA Ship McArthur II to: (1) obtain additional imagery of the seafloor for broader habitat-mapping coverage of sanctuary waters, and (2) help delineate suitable deep-sea coral/sponge habitat, in areas of both high and low commercial-fishing activities, to serve as sites for surveying-in more detail using an ROV on subsequent cruises. Several regions of the sea floor throughout the OCNMS were surveyed and mosaicked at 1-meter pixel resolution. Imagery from the side scan sonar mapping efforts was integrated with other complementary data from a towed camera sled, ROVs, sedimentary samples, and bathymetry records to describe geological and biological (where possible) aspects of habitat. Using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999), we created a preliminary map of various habitat polygon features for use in a geographical information system (GIS). This report provides a description of the mapping and groundtruthing efforts as well as results of the image classification procedure for each of the areas surveyed. (PDF contains 60 pages.)

Olympic Coast National Marine Sanctuary Habitat Mapping: Survey report and classification of side scan sonar data from surveys HMPR-114-2004-02 and HMPR-116-2005-01.

The Olympic Coast National Marine Sanctuary (OCNMS) continues to invest significant resources into seafloor mapping activities along Washington’s outer coast (Intelmann and Cochrane 2006; Intelmann et al. 2006; Intelmann 2006). Results from these annual mapping efforts offer a snapshot of current ground conditions, help to guide research and management activities, and provide a baseline for assessing the impacts of various threats to important habitat. During the months of August 2004 and May and July 2005, we used side scan sonar to image several regions of the sea floor in the northern OCNMS, and the data were mosaicked at 1-meter pixel resolution. Video from a towed camera sled, bathymetry data, sedimentary samples and side scan sonar mapping were integrated to describe geological and biological aspects of habitat. Polygon features were created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). For three small areas that were mapped with both side scan sonar and multibeam echosounder, we made a comparison of output from the classified images indicating little difference in results between the two methods. With these considerations, backscatter derived from multibeam bathymetry is currently a costefficient and safe method for seabed imaging in the shallow (<30 meters) rocky waters of OCNMS. The image quality is sufficient for classification purposes, the associated depths provide further descriptive value and risks to gear are minimized. In shallow waters (<30 meters) which do not have a high incidence of dangerous rock pinnacles, a towed multi-beam side scan sonar could provide a better option for obtaining seafloor imagery due to the high rate of acquisition speed and high image quality, however the high probability of losing or damaging such a costly system when deployed as a towed configuration in the extremely rugose nearshore zones within OCNMS is a financially risky proposition. The development of newer technologies such as intereferometric multibeam systems and bathymetric side scan systems could also provide great potential for mapping these nearshore rocky areas as they allow for high speed data acquisition, produce precisely geo-referenced side scan imagery to bathymetry, and do not experience the angular depth dependency associated with multibeam echosounders allowing larger range scales to be used in shallower water. As such, further investigation of these systems is needed to assess their efficiency and utility in these environments compared to traditional side scan sonar and multibeam bathymetry. (PDF contains 43 pages.)